On Tue, Mar 30, 2004, Skauge Tormod wrote:
>
> I'm trying to run a simulation of a RNA in vacuum. As recommended in the
> amber DNA tutorial, I want to include a larger and softer counterion
> than Na+ and have tried K+ and IB. Running sander for the heating
> process (to 300K) fails with the comment "bad atom symbol: I" or "bad
> atom symbol: K".
.....
>
> The "testrun" file:
> test to see if IB and K+ works
>
> &cntrl
> IMIN=0, NTX=1, IREST=0, NSNB=99999,
> TIMLIM=300, IG=71277, IBELLY=0,
> IGB=1, NTB=0, GBPARM=2, GBSA=0,
^^^^^^
You say that you want to run RNA in vacuum (which I don't think is _really_
recommended in the DNA tutorial or anywhere else), yet you set igb=1, which
requests a generalized Born simulation. GB simulations are not set up to use
counterions, as counterions are treated as a part of the solvent, not part of
the solute.
You could set igb=0 to indeed get a vacuum simulation, but I cannot in good
conscience actually recommend this. Either using an explicit water or a
generalized Born model should be much better.
.....dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Wed Mar 31 2004 - 19:53:00 PST
